I'm pretty certain Thessaloniki was the most important Byzantine city in Europe, given that it was second in population only to Constantinople and Thessaloniki, unlike some other cities, has remained under Byzantine rule all the way to the 13th century.

I know Antioch was certainly no.2 in terms of size(Tertius chandler's book details what the largest cities on earth were at different times and the top 5-10 is freely accessible online and Antioch was consistently in the top 5 Western cities from it's foundation by it's Seleucid namesake deep into the Middle Ages) by a pretty wide margin. Athens and Corinith were among the largest cities on earth during the 5th century BC(and Corinith maybe a few centuries later?) and never recovered their centrality after the various sacking and plagues they'd sustained at their height, this was about a millenia later. The other one's were never amongst the world's largest cities. Constantinople of course was consistently the West's largest or occasionally second largest city from Constantine all the way to the industrial revolution when London and Paris finally caught it. I'm going to make a strong guess that Niceaea was third given that this is where the government went during the aftermath of the Fourth Crusade.

It really depends on when you're talking about. In late antiquity the 'big three' were Constantinople, Antioch, and Alexandria, which all retained populations consistently in the hundreds of thousands, followed by cities like Ephesus (which got a new aqueduct in the 6th century), Thessalonica, Nicomedia, Carthage, Athens, Rome, etc. In the early middle Byzantine period Constantinople became increasingly exceptional within the empire as a large city with classical institutions, hierarchies, and urban spaces, only really joined in that level of continuity by Thessalonica. Other significant centers of the period include, in no particular order, Adrianople, Attaleia, Nicomedia, Iconion, Caesarea, and Amorion before it was destroyed in the mid 9th century. By the late 10th century the situation had changed again, although not nearly as drastically as in the 7th, and, though Constantinople was still absolutely exceptional as the Roman megalopolis, major urban centers were once again asserting themselves away from the Bosporus. Thessalonica still retained its position as the empire's second city, but the newly reconquered and rechristianized Antioch followed not far behind, at populations of around 100-130,000 and 70-80,000 respectively, and Greece especially, recently made safe, saw major investment and growth. Other major centers of the 10th and 11th centuries, with populations of around 30-60 thousand, include, in no particular order, Iconion, Caesarea, Corinth, Ancyra, Adrianople, Attaleia, Nicomedia, Bari, Chonai, Tarsus, and Edessa, among others. For the 20 years it was under Roman control, Ani, capital of Armenia, also likely became the fourth city of the empire, with a population of around 60-70 thousand, possibly a bit more.

Not much changed entering the Komnenian period, aside from the loss of a number of major cities in Anatolia and Italy, most notably Antioch, Iconion, and Caesarea. Constantinople remained the largest Roman city by an order of magnitude, followed by Thessalonica, Corinth, Adrianople, Nicomedia, Chonai, etc. The early 13th century saw a massive decline in the population of Constantinople, pushing it below Thessalonica from 1204 into the 1260's and maybe even 70's, and the rise of Nicaea as the capital of the empire in exile, accompanied by the loss of Athens and Corinth to western lords. The mid-late 13th century saw a stabilization towards something resembling previous norms, with Constantinople reasserting itself as the empire's first city, albeit followed closely by Thessalonica, behind which again trailed Nicaea, Adrianople, and Nicomedia. Finally, Nicaea, Nicomedia, and Thessalonica were lost in succession during the 14th and 15th centuries, leaving Constantinople and Corinth, which had been recovered in 1403, as the empire's sole cities up to 1453.

I agree with Jean completely that Thessalonika was number #2 after the Arab conquests. Indeed, one wonders at certain points the degree to which the city was de facto independent and justifying some of its actions in the its hinterland vis-a-vis Avars and Slavs through the cult of St Demetrios, as recorded in the miracles of St Demetrios. But that argument shouldn't be taken too far, and has yet to be comprehensively made. In the 12th century Thessalonika seems to have taken on a new importance in rivaling Constantinople to some degree. We see elites sending their children there for education rather than Constantinople.

Archaeology has a big role to play in understanding urban centres in the Byzantine world. Ephesos remained important, but seems to have become poly-centric. The excavations at Amorion have revealed a substantial city with most of the classical amenities, including baths and workshops. Work at Euchaita has similarly shown a more substantial settlement area than previously supposed. Attaleia was probably the most important Mediterranean emporion but we don't know that much about it. Long considered a marginal and economically un-productive region, aechaeology has turned around our views on Cappadocia. Some of the underground settlements housed thousands.

I think Byzantine Caesarea was also an important city in Anatolia, it must have also been a center of culture as well. If I remember correctly in the 9th-10th century Arethas had bought a manuscript of Phaedrus of Plato from Caesarea if I remember correctly. So there must have been some intellectual activity, possibly,

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